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I has been using RosettaRemodel
-remodel:domainFusion:insert_segment_from_pdb for connecting pdb files such as connecting 1 helix pdb file and another 1 helix pdb file.
But it doesnt always work, is there another way to connecting two helices in different pdb file by loop?
Im wondering what protocols can be used for connecting two pdb files with loop to generate 1 pdb file
please help me
Hello, I would like to ask for some help, regarding the article Kemp elimination catalysts by computational enzyme design, you would still have the transition state calculated by gauss, I need the output because I am trying to replicate the article, and I need the coordinates of the hydrogen being removed from the carbon in the transition state. Does anyone have these outputs?
Att. Thank you
I am doing semi-rational design of my protein. So far I have one mutation that increases thermostability identified in vitro. However, Rosetta didn't predict this mutation in pmut scan. When I scored the protein variant with this mutation, the score was better than all the mutations predicted by Rosetta.
I want to evaluate the ddg between WT and disulfide bond mutants
1. I try to use ddg_monomer and fond it does not suport it
2. Then I build disulfide bond mutants with moddler, and then try to use ddg_monomer to evaluate the ddg ( mutant CYS recovery to the amino acid of WT), and it does not work , too.
3. Just as 2. I try to use another APP, cartesian_ddg ， and disulfide bond mutants as the star model，and ddgs seem is similar(just try three mutant)
I'm following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I'm in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault.
I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).
How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!
Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?
Best and thank for any help,
I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation , I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31” it shows there is no parameters for C-N-C-CA
I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsions (i.e., importing 0 1 180.00 for related parameter in mm_torsion_params.txt)